I have this too and I'm stage 3/tuned. it happens in 1st and 2nd for me normally only on a very flat stretch of road.

Has this always been a problem or a recent development?

I think it might be the ecu alternating back and forth between cells in one of the map's parameters because all conditions are being held right on the transition point (be it load, rpm, etc.). The difference between the two cells must be so different that it causes the bucking.

Edit: ^^This is just a guess, I believe the ecu interpolates the values in between the cells but maybe there is a condition where the transition isn't smooth...